Mercurial > repos > nilesh > rseqc

diff read_duplication.xml @ 13:a7f9084572fe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rseqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
author iuc
date Sat, 10 Dec 2022 11:21:47 +0000
parents 57fad5deeb8e
children b21f0167e197
line wrap: on
line diff
--- a/read_duplication.xml	Sat Dec 18 19:40:16 2021 +0000
+++ b/read_duplication.xml	Sat Dec 10 11:21:47 2022 +0000
@@ -1,9 +1,9 @@
-<tool id="rseqc_read_duplication" name="Read Duplication" version="@TOOL_VERSION@">
+<tool id="rseqc_read_duplication" name="Read Duplication" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
     <description>determines reads duplication rate with sequence-based and mapping-based strategies</description>
-    <expand macro="bio_tools"/>
     <macros>
         <import>rseqc_macros.xml</import>
     </macros>
+    <expand macro="bio_tools"/>
 
     <expand macro="requirements" />
 
@@ -12,7 +12,8 @@
     <version_command><![CDATA[read_duplication.py --version]]></version_command>
 
     <command><![CDATA[
-        read_duplication.py -i '${input}' -o output -u ${upLimit} -q ${mapq}
+        @BAM_SAM_INPUTS@
+        read_duplication.py -i 'input.${extension}' -o output -u ${upLimit} -q ${mapq}
         ]]>
     </command>
 
@@ -24,10 +25,10 @@
     </inputs>
 
     <outputs>
-        <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf" />
-        <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position xls)"/>
-        <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence xls)"/>
-        <expand macro="rscript_output_data" filename="output.DupRate_plot.r" />
+        <expand macro="pdf_output_data" filename="output.DupRate_plot.pdf"  label="${tool.name} on ${on_string}: plot (PDF)"/>
+        <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string}: positon (XLS)"/>
+        <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string}: sequences (XLS)"/>
+        <expand macro="rscript_output_data" filename="output.DupRate_plot.r" label="${tool.name} on ${on_string}: Rscript"/>
     </outputs>
 
     <tests>